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Concept: Capra

141

This experiment was aimed to determine proper physical traits in the diet for goats by investigating the effects of physically effective neutral detergent fiber (peNDF) content on dry matter intake (DMI), digestibility, and chewing activity in black goats fed with total mixed ration (TMR).

Concepts: Energy, Chemistry, Thermodynamics, Cheese, Goat, Diet of Japan, Capra, Goats

21

The evolutionary basis of domestication has been a longstanding question and its genetic architecture is becoming more tractable as more domestic species become genome-enabled. Before becoming established worldwide, sheep and goats were domesticated in the fertile crescent 10,500 years before present (YBP) where their wild relatives remain. Here we sequence the genomes of wild Asiatic mouflon and Bezoar ibex in the sheep and goat domestication center and compare their genomes with that of domestics from local, traditional, and improved breeds. Among the genomic regions carrying selective sweeps differentiating domestic breeds from wild populations, which are associated among others to genes involved in nervous system, immunity and productivity traits, 20 are common to Capra and Ovis. The patterns of selection vary between species, suggesting that while common targets of selection related to domestication and improvement exist, different solutions have arisen to achieve similar phenotypic end-points within these closely related livestock species.

Concepts: Gene, Genetics, Natural selection, Livestock, Neolithic, Domestic sheep, Ovis, Capra

13

Recently, comparative research on the mechanisms and species-specific adaptive values of attributing attentive states and using communicative cues has gained increased interest, particularly in non-human primates, birds, and dogs. Here, we investigate these phenomena in a farm animal species, the dwarf goat (Capra aegagrus hircus). In the first experiment, we investigated the effects of different human head and body orientations, as well as human experimenter presence/absence, on the behaviour of goats in a food-anticipating paradigm. Over a 30-s interval, the experimenter engaged in one of four different postures or behaviours (head and body towards the subject-‘Control’, head to the side, head and body away from the subject, or leaving the room) before delivering a reward. We found that the level of subjects' active anticipatory behaviour was highest in the control condition and decreased with a decreasing level of attention paid to the subject by the experimenter. Additionally, goats ‘stared’ (i.e. stood alert) at the experimental set-up for significantly more time when the experimenter was present but paid less attention to the subject (‘Head’ and ‘Back’ condition) than in the ‘Control’ and ‘Out’ conditions. In a second experiment, the experimenter provided different human-given cues that indicated the location of a hidden food reward in a two-way object choice task. Goats were able to use both ‘Touch’ and ‘Point’ cues to infer the correct location of the reward but did not perform above the level expected by chance in the ‘Head only’ condition. We conclude that goats are able to differentiate among different body postures of a human, including head orientation; however, despite their success at using multiple physical human cues, they fail to spontaneously use human head direction as a cue in a food-related context.

Concepts: Psychology, Human, Mammal, Primate, Livestock, Goat, Capra, Goats

9

The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus) based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced what is, to our knowledge, the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps. Our assembly represents a ∼400-fold improvement in continuity due to properly assembled gaps, compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex yet produced for an individual of a ruminant species.

Concepts: DNA, Milk, Mammal, Livestock, Ruminant, Goat, Capra, Goats

5

1.Selective hunting can affect demographic characteristics and phenotypic traits of the targeted species. Hunting systems often involve harvesting quotas based on sex, age and/or size categories to avoid selective pressure. However, it is difficult to assess if such regulations deter hunters from targeting larger ‘trophy’ animals with longer horns that may have evolutionary consequences. 2.Here, we compile 44'088 annually resolved and absolutely dated measurements of Alpine ibex (Capra ibex) horn growth increments from 8'355 males, harvested between 1978 and 2013, in the eastern Swiss Canton of Grisons. We aim to determine if male ibex with longer horns were preferentially targeted, causing animals with early rapid horn growth to have shorter lives, and whether such hunting selection translated into long-term trends in horn size over the past four decades. 3.Results show that medium- to longer-horned adult males had a higher probability of being harvested than shorter-horned individuals of the same age, and that regulations do affect the hunters' behaviour. Nevertheless, phenotypic traits like horn length, as well as body size and weight, remained stable over the study period. 4.Though selective trophy hunting still occurs, it did not cause a measurable evolutionary response in Grisons' Alpine ibex populations; managed and surveyed since 1978. Nevertheless, further research is needed to understand if phenotypic trait development is co-influenced by other, potentially compensatory factors that may possibly mask the effects of selective, long-term hunting pressure. This article is protected by copyright. All rights reserved.

Concepts: Natural selection, Switzerland, Hunting, Copyright, Cantons of Switzerland, Horn, Capra, Graubünden

5

Bronchopneumonia is a population limiting disease of bighorn sheep (Ovis canadensis) that has been associated with contact with domestic Caprinae. The disease is polymicrobial but is initiated by Mycoplasma ovipneumoniae, which is commonly carried by both domestic sheep (O. aries) and goats (Capra aegagrus hircus). However, while previous bighorn sheep comingling studies with domestic sheep have resulted in nearly 100% pneumonia mortality, only sporadic occurrence of fatal pneumonia was reported from previous comingling studies with domestic goats. Here, we evaluated the ability of domestic goats of defined M. ovipneumoniae carriage status to induce pneumonia in comingled bighorn sheep.

Concepts: Livestock, Goat, Domestic sheep, Ovis, Capra, Mouflon, Bighorn Sheep, Goats

3

High-throughput sequencing is a powerful tool, but suffers biases and errors that must be accounted for to prevent false biological conclusions. Such errors include batch effects, technical errors only present in subsets of data due to procedural changes within a study. If overlooked and multiple batches of data are combined, spurious biological signals can arise, particularly if batches of data are correlated with biological variables. Batch effects can be minimized through randomisation of sample groups across batches. However, in long-term or multi-year studies where data are added incrementally, full randomisation is impossible and batch effects may be a common feature. Here we present a case study where false signals of selection were detected due to a batch effect in a multi-year study of Alpine ibex (Capra ibex). The batch effect arose because sequencing read length changed over the course of the project and populations were added incrementally to the study, resulting in non-random distributions of populations across read lengths. The differences in read length caused small misalignments in a subset of the data, leading to false variant alleles and thus false SNPs. Pronounced allele frequency differences between populations arose at these SNPs because of the correlation between read length and population. This created highly statistically significant, but biologically spurious, signals of selection and false associations between allele frequencies and the environment. We highlight the risk of batch effects and discuss strategies to reduce the impacts of batch effects in multi-year high-throughput sequencing studies. This article is protected by copyright. All rights reserved.

Concepts: Gene, Genetics, Evolution, Biology, Genetic genealogy, Population genetics, Allele frequency, Capra

1

Restoration of lost species ranges to their native distribution is key for the survival of endangered species. However, reintroductions often fail and long-term genetic consequences are poorly understood. Alpine ibex (Capra ibex) are wild goats that recovered from <100 individuals to ~50,000 within a century by population reintroductions. We analyzed the population genomic consequences of the Alpine ibex reintroduction strategy. We genotyped 101,822 genomewide single nucleotide polymorphism loci in 173 Alpine ibex, the closely related Iberian ibex (Capra pyrenaica) and domestic goat (Capra hircus). The source population of all Alpine ibex maintained genetic diversity comparable to Iberian ibex, which experienced less severe bottlenecks. All reintroduced Alpine ibex populations had individually and combined lower levels of genetic diversity than the source population. The reintroduction strategy consisted of primary reintroductions from captive breeding and secondary reintroductions from established populations. This stepwise reintroduction strategy left a strong genomic footprint of population differentiation, which increased with subsequent rounds of reintroductions. Furthermore, analyses of genomewide runs of homozygosity showed recent inbreeding primarily in individuals of reintroduced populations. We showed that despite the rapid census recovery, Alpine ibex carry a persistent genomic signature of their reintroduction history. We discuss how genomic monitoring can serve as an early indicator of inbreeding.

Concepts: Genetics, Bioinformatics, Population genetics, Goat, Megafauna of Eurasia, Mammals of Europe, Capra, Goats

1

Variation in common personality traits, such as boldness or exploration, is often associated with risk-reward trade-offs and behavioural flexibility. To date, only a few studies have examined the effects of consistent behavioural traits on both learning and cognition. We investigated whether certain personality traits (‘exploration’ and ‘sociability’) of individuals were related to cognitive performance, learning flexibility and learning style in a social ungulate species, the goat (Capra hircus). We also investigated whether a preference for feature cues rather than impaired learning abilities can explain performance variation in a visual discrimination task. We found that personality scores were consistent across time and context. Less explorative goats performed better in a non-associative cognitive task, in which subjects had to follow the trajectory of a hidden object (i.e. testing their ability for object permanence). We also found that less sociable subjects performed better compared to more sociable goats in a visual discrimination task. Good visual learning performance was associated with a preference for feature cues, indicating personality-dependent learning strategies in goats. Our results suggest that personality traits predict the outcome in visual discrimination and non-associative cognitive tasks in goats and that impaired performance in a visual discrimination tasks does not necessarily imply impaired learning capacities, but rather can be explained by a varying preference for feature cues.

Concepts: Psychology, Cognitive psychology, Cognition, Educational psychology, Explanation, Behaviorism, Goat, Capra

1

Using a comparative approach, we investigated the ability of dwarf goats and sheep to use direct and indirect information about the location of a food reward in an object-choice task. Subjects had to choose between two cups with only one covering a reward. Before making a choice, subjects received information about the baited (direct information) or non-baited cup (indirect information). Both goats and sheep were able to use direct information (presence of food) in the object choice task. After controlling for local enhancement, we found that goats rather than sheep were able to use indirect information (i.e., the absence of food) to find a reward. The actual test setup could not clarify whether individual goats were able to inferentially reason about the content of the baited cup when only shown the content of the non-baited cup or if they simply avoided the empty cup in that situation. As browsing species, feral and wild goats exhibit highly selective feeding behaviour compared to the rather unselective grazing sheep. The potential influence of this species-specific foraging flexibility of goats and sheep for using direct and indirect information to find a food reward is discussed in relation to a higher aversion to losses in food acquisition in goats compared to sheep.

Concepts: Livestock, Goat, Domestic sheep, Ovis, Capra, Goats, Wild goat